rs1430509

Variant names:

• chr4-64811729-A-G
• rs1430509
• XR_001741711.2:n.204+36904A>G

Your query was ambiguous. Multiple possible variants found:

• chr4-64811729-A-G
• chr4-64811729-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001741711.2(LOC107986284):​n.204+36904A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 151,092 control chromosomes in the GnomAD database, including 868 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.10 (868 hom., cov: 32)
• Consequence: LOC107986284 XR_001741711.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.86
• Publications: 1 publications found

Genes affected

LOC107986284 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986284	XR_001741711.2	n.204+36904A>G		intron_variant	Intron 1 of 2
LOC107986284	XR_001741712.2	n.383+35685A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15509 AN: 150982 Hom.: 863 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.0818

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.0945

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.0753

Gnomad MID AF: 0.179

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.112

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.103 AC: 15539 AN: 151092 Hom.: 868 Cov.: 32 AF XY: 0.102 AC XY: 7525 AN XY: 73788

African (AFR) AF: 0.103 AC: 4241 AN: 41144

American (AMR) AF: 0.0817 AC: 1235 AN: 15116

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 503 AN: 3466

East Asian (EAS) AF: 0.0947 AC: 484 AN: 5110

South Asian (SAS) AF: 0.150 AC: 718 AN: 4782

European-Finnish (FIN) AF: 0.0753 AC: 778 AN: 10338

Middle Eastern (MID) AF: 0.179 AC: 52 AN: 290

European-Non Finnish (NFE) AF: 0.104 AC: 7078 AN: 67832

Other (OTH) AF: 0.118 AC: 248 AN: 2104

Alfa AF: 0.106 Hom.: 498

Bravo AF: 0.100

Asia WGS AF: 0.150 AC: 523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.3
DANN	Benign	0.71
PhyloP100		1.9

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1430509; hg19: chr4-65677447;